[gmx-users] struggles with cyclic peptides

Justin Lemkul jalemkul at vt.edu
Mon Sep 14 13:03:29 CEST 2015

On 9/14/15 6:58 AM, Nikhil wrote:
> Hi Justin,
> So your saying working with Gromacs for cyclic peptide is hopeless using
> available methods?

I don't see a way to do it.

> i tried all terminals
> in  .tdb file  removing C ,O and H from -COOH so that only O will add up
> and before that removing O from the pdb ,i tired that but ends up with
> lots of errors.
> i found in archives same issues as connection establishing with C-N but
> extra atoms at each terminals ..!

Right, in principle, you can generate "normal" termini, delete the unnecessary 
atoms, renumber *everything* in the topology from 1, and write in the bonded 
interactions (bonds, angles, dihedrals) and it will work.  That's a lot of 
effort and is very error prone.

One possibility, since you want to use CHARMM, is to use CHARMM-GUI to set 
things up.  It is quite straightforward and supports cyclic peptides.  Our 
latest version of the server provides all GROMACS topology and input files for 
doing the run.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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